Re: GBIS and hydrophobic term, in replay to Jerome and David discussion

From: Branko (
Date: Sun Oct 23 2011 - 09:55:27 CDT

I agree Jerome,

When find some time, I'll try with longer tail alcohol, for example
n-octanol. Still whole discussion is obviously useful if one want to use
pure hydrocarbon (partition coefficient alkan/water is always actual)
as a solvent - maybe serious discrepancy could arise using impl solvation.

Kind regards


On 10/23/2011 4:43 PM, Jérôme Hénin wrote:
> Hi Branko,
> This is good news, but not very surprising since EtOH has weaker
> self-interactions than water, hence a much smaller cavitation free
> energy and "ethanolphobic effect".
> Best,
> Jerome
> On 23 October 2011 16:36, Branko<> wrote:
>> Jerome, David,
>> After your discussion on hydrophobic term in GBIS, I compare my simulations
>> using expl. and impl. EtOH with one small flexible molecule (as a part of
>> ongoing study). Indeed free-energy surface, obtained by ABF (Jerome topic)
>> looks different, providing that more conformation have a lower energy, but
>> shape of the surfaces is a same. More importantly global minima are very
>> comparable. Conformation sampling is also very, very similar (I use one
>> distance, previously chosen as a colvar, which in reasonable way describe
>> conformational change). Plot of ~ 40 conformational clusters from exp. vs.
>> same no of clusters obtained by impl. solvation give r = 0.98. Molecule
>> under simulation can be described as amphyphylic, having one hydrofobic end
>> and other with two carboxylates, so during simulation hydrophobic
>> interactions could be considered as non-negligible.
>> So looks that by implicit solvation one can obtain something 'lower energy
>> content' in vast majority of samples, but structurally results are very
>> similar.
>> Branko
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